标题: 如何回复动力学模拟是否要做三次重复疑问 [打印本页] 作者Author: xiaoai 时间: yesterday 17:36 标题: 如何回复动力学模拟是否要做三次重复疑问 工作中做了几个突变的蛋白质复合体的300ns动力学模拟
意见中有一条
Molecular Dynamics Simulations - Robustness and Interpretation: The 300 ns MD simulations conducted for each mutant and wild type are noteworthy in duration, and the analyses performed, including RMSD, RMSF, SASA, hydrogen bonds, and PCA, are suitably implemented. Nonetheless:
The simulations seem to have been conducted in single replicates, indicating a need for greater statistical rigor. The authors are encouraged to elucidate whether replicates were conducted and, in the absence thereof, to provide a rationale for the adequacy of a singular trajectory.
如果没做平行模拟，那建议按审稿人要求做一下（这是如今很多期刊的基本要求，不做的话审稿人那很可能过不去）。然后引用一些做了平行模拟的文献（如J. Chem. Inf. Model. 2020, 60, 4, 2189–2198这篇做了三次平行模拟，“For each protein-ligand complex, we ran 3 × 100 ns production runs, each started with the same initial structure but using different initial velocity random seeds.”）。
做完后从各种参数对比下三次模拟的相似程度（也就是可重复性，比如SASA，氢键数量，寿命等）来确认模拟结果的合理性，证明模拟结果并非偶然结果。回复审稿人意见时直接回复你做了平行模拟并说一下轨迹的可重复性就行了。